template update to v3.1.1 (#15)

* add author to enable pipeline sync * Template update for nf-core/tools version 3.1.1 * correct Changelog * correct Changelog * GATK in igenomes * revert changes that do not belong to template update * revert changes that do not belong to template update * fix yml * prettier * update tests * fix: indentation * Apply suggestions from code review Co-authored-by: Mark Polster <[email protected]> --------- Co-authored-by: Mark Polster <[email protected]>
qbic-pipelines · Jan 10, 2025 · 9dc69a0 · 9dc69a0
1 parent 297e6b4
commit 9dc69a0
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diff --git a/.editorconfig b/.editorconfig
@@ -31,3 +31,7 @@ indent_size = unset
 # ignore python and markdown
 [*.{py,md}]
 indent_style = unset
+
+# ignore ro-crate metadata files
+[**/ro-crate-metadata.json]
+insert_final_newline = unset
diff --git a/.github/workflows/download_pipeline.yml b/.github/workflows/download_pipeline.yml
@@ -28,8 +28,12 @@ env:
   NXF_ANSI_LOG: false
 
 jobs:
-  download:
+  configure:
     runs-on: ubuntu-latest
+    outputs:
+      REPO_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPO_LOWERCASE }}
+      REPOTITLE_LOWERCASE: ${{ steps.get_repo_properties.outputs.REPOTITLE_LOWERCASE }}
+      REPO_BRANCH: ${{ steps.get_repo_properties.outputs.REPO_BRANCH }}
     steps:
       - name: Install Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -53,65 +57,70 @@ jobs:
           pip install git+https://github.com/nf-core/tools.git@dev
 
       - name: Get the repository name and current branch set as environment variable
+        id: get_repo_properties
         run: |
-          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> ${GITHUB_ENV}
-          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> ${GITHUB_ENV}
-          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> ${GITHUB_ENV}
+          echo "REPO_LOWERCASE=${GITHUB_REPOSITORY,,}" >> "$GITHUB_OUTPUT"
+          echo "REPOTITLE_LOWERCASE=$(basename ${GITHUB_REPOSITORY,,})" >> "$GITHUB_OUTPUT"
+          echo "REPO_BRANCH=${{ github.event.inputs.testbranch || 'dev' }}" >> "$GITHUB_OUTPUT"
 
       - name: Make a cache directory for the container images
         run: |
           mkdir -p ./singularity_container_images
 
+  download:
+    runs-on: ubuntu-latest
+    needs: configure
+    steps:
       - name: Download the pipeline
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
         run: |
-          nf-core pipelines download ${{ env.REPO_LOWERCASE }} \
-          --revision ${{ env.REPO_BRANCH }} \
-          --outdir ./${{ env.REPOTITLE_LOWERCASE }} \
+          nf-core pipelines download ${{ needs.configure.outputs.REPO_LOWERCASE }} \
+          --revision ${{ needs.configure.outputs.REPO_BRANCH }} \
+          --outdir ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }} \
           --compress "none" \
           --container-system 'singularity' \
           --container-library "quay.io" -l "docker.io" -l "community.wave.seqera.io/library/" \
           --container-cache-utilisation 'amend' \
           --download-configuration 'yes'
 
       - name: Inspect download
-        run: tree ./${{ env.REPOTITLE_LOWERCASE }}
+        run: tree ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}
 
       - name: Count the downloaded number of container images
         id: count_initial
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Initial container image count: $image_count"
-          echo "IMAGE_COUNT_INITIAL=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_INITIAL=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Run the downloaded pipeline (stub)
         id: stub_run_pipeline
         continue-on-error: true
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
       - name: Run the downloaded pipeline (stub run not supported)
         id: run_pipeline
-        if: ${{ job.steps.stub_run_pipeline.status == failure() }}
+        if: ${{ steps.stub_run_pipeline.outcome == 'failure' }}
         env:
           NXF_SINGULARITY_CACHEDIR: ./singularity_container_images
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ needs.configure.outputs.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ needs.configure.outputs.REPO_BRANCH }}) -profile test,singularity --outdir ./results
 
       - name: Count the downloaded number of container images
         id: count_afterwards
         run: |
           image_count=$(ls -1 ./singularity_container_images | wc -l | xargs)
           echo "Post-pipeline run container image count: $image_count"
-          echo "IMAGE_COUNT_AFTER=$image_count" >> ${GITHUB_ENV}
+          echo "IMAGE_COUNT_AFTER=$image_count" >> "$GITHUB_OUTPUT"
 
       - name: Compare container image counts
         run: |
-          if [ "${{ env.IMAGE_COUNT_INITIAL }}" -ne "${{ env.IMAGE_COUNT_AFTER }}" ]; then
-            initial_count=${{ env.IMAGE_COUNT_INITIAL }}
-            final_count=${{ env.IMAGE_COUNT_AFTER }}
+          if [ "${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}" -ne "${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}" ]; then
+            initial_count=${{ steps.count_initial.outputs.IMAGE_COUNT_INITIAL }}
+            final_count=${{ steps.count_afterwards.outputs.IMAGE_COUNT_AFTER }}
             difference=$((final_count - initial_count))
             echo "$difference additional container images were \n downloaded at runtime . The pipeline has no support for offline runs!"
             tree ./singularity_container_images

diff --git a/.nf-core.yml b/.nf-core.yml
@@ -1,34 +1,34 @@
 lint:
+  actions_ci: false
   files_exist:
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-vcftomat_logo_light.png
-  - docs/images/nf-core-vcftomat_logo_light.png
-  - docs/images/nf-core-vcftomat_logo_dark.png
-  - .github/ISSUE_TEMPLATE/config.yml
-  - .github/workflows/awstest.yml
-  - .github/workflows/awsfulltest.yml
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-vcftomat_logo_light.png
+    - docs/images/nf-core-vcftomat_logo_light.png
+    - docs/images/nf-core-vcftomat_logo_dark.png
+    - .github/ISSUE_TEMPLATE/config.yml
+    - .github/workflows/awstest.yml
+    - .github/workflows/awsfulltest.yml
   files_unchanged:
-  - .github/CONTRIBUTING.md
-  - .prettierignore
-  - .github/CONTRIBUTING.md
-  - .prettierignore
-  - CODE_OF_CONDUCT.md
-  - assets/nf-core-vcftomat_logo_light.png
-  - docs/images/nf-core-vcftomat_logo_light.png
-  - docs/images/nf-core-vcftomat_logo_dark.png
-  - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/CONTRIBUTING.md
+    - .prettierignore
+    - .github/CONTRIBUTING.md
+    - .prettierignore
+    - CODE_OF_CONDUCT.md
+    - assets/nf-core-vcftomat_logo_light.png
+    - docs/images/nf-core-vcftomat_logo_light.png
+    - docs/images/nf-core-vcftomat_logo_dark.png
+    - .github/ISSUE_TEMPLATE/bug_report.yml
   included_configs: false
-  actions_ci: false
   multiqc_config:
-  - report_comment
+    - report_comment
   nextflow_config:
-  - manifest.name
-  - manifest.homePage
-  - validation.help.beforeText
-  - validation.help.afterText
-  - validation.summary.beforeText
-  - validation.summary.afterText
-nf_core_version: 3.1.0
+    - manifest.name
+    - manifest.homePage
+    - validation.help.beforeText
+    - validation.help.afterText
+    - validation.summary.beforeText
+    - validation.summary.afterText
+nf_core_version: 3.1.1
 repository_type: pipeline
 template:
   author: "Famke Bäuerle, Dorothy Ellis"
@@ -40,8 +40,8 @@ template:
   org: qbic-pipelines
   outdir: .
   skip_features:
-  - gitpod
-  - codespaces
-  - fastqc
-  - adaptivecard
+    - gitpod
+    - codespaces
+    - fastqc
+    - adaptivecard
   version: 1.2.0dev
diff --git a/.prettierignore b/.prettierignore
@@ -9,3 +9,4 @@ testing/
 testing*
 *.pyc
 bin/
+ro-crate-metadata.json
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,18 +5,20 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## v1.2.0dev
 
-### Added
+### `Added`
 
-### Fixed
+### `Fixed`
+
+- [#15](https://github.com/qbic-pipelines/vcftomat/pull/15) - template update to v3.1.1
 
 ## v1.1.0 - Newton Puccoon - 08.01.2025
 
-### Added
+### `Added`
 
 - [#7](https://github.com/qbic-pipelines/vcftomat/pull/7) - samplenames to columns
 - [#8](https://github.com/qbic-pipelines/vcftomat/pull/8) - concat for sample, label pairs
 
-### Fixed
+### `Fixed`
 
 - [#5](https://github.com/qbic-pipelines/vcftomat/pull/5) - filename collision
 - [#10](https://github.com/qbic-pipelines/vcftomat/pull/10) - prepare release 1.1.0

diff --git a/LICENSE b/LICENSE
@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) Famke Bäuerle, Dorothy Ellis
+Copyright (c) The qbic-pipelines/vcftomat team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
@@ -1,6 +1,6 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/qbic-pipelines/vcftomat/tree/dev"
-  target="_blank">qbic-pipelines/vcftomat</a> analysis pipeline.
+  This report has been generated by the <a href="https://github.com/qbic-pipelines/vcftomat/tree/dev" target="_blank">qbic-pipelines/vcftomat</a>
+  analysis pipeline.
 report_section_order:
   "qbic-pipelines-vcftomat-methods-description":
     order: -1000

diff --git a/conf/test.config b/conf/test.config
@@ -22,6 +22,5 @@ params {
     config_profile_name        = 'Test profile'
     config_profile_description = 'Minimal test dataset to check pipeline function. Skips processes GATK_GENOTYPEGVCFS and BCFTOOLS_MERGE.'
 
-    // Input data
     input  = "${projectDir}/tests/input.csv"
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -14,7 +14,7 @@ params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    // Input data
+    // Input data for full size test
     input  = "${projectDir}/tests/input-full.csv"
 
     // Genome references

diff --git a/nextflow.config b/nextflow.config
@@ -38,13 +38,14 @@ params {
     show_hidden                  = false
     version                      = false
     pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/'
-    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-    config_profile_name          = null
-    config_profile_description   = null
-    custom_config_version        = 'master'
-    custom_config_base           = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    config_profile_contact       = null
-    config_profile_url           = null
+    trace_report_suffix          = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
+    config_profile_name        = null
+    config_profile_description = null
+
+    custom_config_version      = 'master'
+    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
+    config_profile_contact     = null
+    config_profile_url         = null
 
     // Schema validation default options
     validate_params              = true
@@ -148,14 +149,16 @@ profiles {
         wave.freeze             = true
         wave.strategy           = 'conda,container'
     }
-
     test      { includeConfig 'conf/test.config'      }
     test_full { includeConfig 'conf/test_full.config' }
 }
 
 // Load nf-core custom profiles from different Institutions
 includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
 
+// Load qbic-pipelines/vcftomat custom profiles from different institutions.
+// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/vcftomat.config" : "/dev/null"
+
 // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
 // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
 // Set to your registry if you have a mirror of containers
@@ -229,6 +232,7 @@ manifest {
             orcid: ''
         ],
     ]
+    author          = "qbic"
     homePage        = 'https://github.com/qbic-pipelines/vcftomat'
     description     = """Nextflow pipeline to convert (g)vcfs to matrices suitable for statistical analysis"""
     mainScript      = 'main.nf'
@@ -251,7 +255,8 @@ validation {
         command = "nextflow run qbic-pipelines/vcftomat -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
         fullParameter = "help_full"
         showHiddenParameter = "show_hidden"
-
     }
 }
-nextflow.enable.moduleBinaries = true
+
+// Load modules.config for DSL2 module specific options
+includeConfig 'conf/modules.config'
-Original file line number
+Diff line change
@@ Expand Up / @@ -9,3 +9,4 @@ testing/ @@
     testing*
     *.pyc
     bin/
+    ro-crate-metadata.json